Disable stock alarm system.

The alarm is integral with the time and alarm control unit, so it cannot be disabled. If you don't use the remote to lock the car, however, it won't set. Try to get in the habit of locking the doors with the manual lock button on the driver's door. Then the alarm won't able, and you can still use the remote to unlock the doors.

Find where the button meets the hood when it is closed. Others have found that the spacing can change over time and trigger the alarm. Supposedly it is adjustable?

my $0.02

The switch isn't *technically* adjustable, but bending the attaching bracket will sometimes do the trick.

After looking in the interior fuse box, I found what kinda looks like a jumper. on one side is says "on" and the other side says "off." I pulled it out and rotated it 180 degrees and pushed it back in and that seems to of worked but the keyless entry and power locks no longer works but the car still starts and everything seems to work. Is this maybe the switch

Not sure what that thing was that you switched since it isn't marked in the owners manual. Hyundaitech?

I went to the garage to see if I could describe the switch better for you. On my US spec Elantra it is a small black plunger syle button. It is located about halfway up the passenger side fender next to the power steering resovoir. If the rubber piece on the hood that pushes the button is missing or worn it won't activate the button.

I was able to set off the alarm by holding it down and locking the car (lights blinked) then taking my finger off the button made it think the hood was opened and set off the siren. If the button isn't pushed when the car is locked the lights don't flash and alarm isn't activated.

You've just disabled some stuff controlled by your time and alarm control unit as well as probably the clock, radio, room lamp, and the door open warning chime. I'd be surprised if your rear window defogger or intermittent wipers work.